I just setup Webby/Compass integration. (https://github.com/Compass/compass/wiki/webby-integration)
Where do I put my Compass/Sass source files, and in what directory do they get output as stylesheets?
You can put your SASS files wherever you want (under the 'content/' directory). So if the directory containing your CSS files is 'content/css', then put them there.
The only important thing is that you set the metadata part correctly, at the top of the SASS file itself. Like this:
$ cat content/css/site.sass
---
filter: sass
extension: css
layout: nil
---
[..cut..]